[ome-devel] Speeding up the TIFF reader in common cases

[Curtis Rueden]

Hi Melissa,

> There is already a ticket for this:

Great! And sorry for forgetting about it. I think the benchmark is a great
way to validate progress on that ticket, too.

Regards,
Curtis


On Thu, Nov 1, 2012 at 2:54 PM, Melissa Linkert <melissa at glencoesoftware.com
> wrote:

> Hi Curtis,
>
> > Johannes & I were discussing how the speed of the Bio-Formats TIFF reader
> > could be improved in common cases. Two main ideas:
>
> There is already a ticket for this:
>
> http://trac.openmicroscopy.org.uk/ome/ticket/9228
>
> You and Johannes were both CC'd when that ticket was created.
> I have updated the ticket to reference this thread.
>
> Regards,
> -Melissa
>
> On Thu, Nov 01, 2012 at 01:39:54PM -0500, Curtis Rueden wrote:
> > Hi all,
> >
> > Johannes & I were discussing how the speed of the Bio-Formats TIFF reader
> > could be improved in common cases. Two main ideas:
> >
> > 1) If the data was written by either ImageJ or Bio-Formats (either which
> > can be detected by examining the first IFD), we could make assumptions
> > about the structure of the pixel data. ImageJ itself does this when
> reading
> > TIFF files (assumes planes are written in contiguous order) which allows
> it
> > to read in TIFFs very quickly. Unfortunately, ImageJ fails to handle
> TIFFs
> > that do not meet these assumptions. But Bio-Formats could fall back to
> its
> > more general parsing logic.
> >
> > 2) Parse IFDs only lazily per plane as each plane is requested, rather
> than
> > fully populating them all up front. AFAIK, the first IFD is really the
> only
> > important one for detecting whether a file should be classified as a
> > particular subtype of TIFF. Also AFAIK, we would still need to walk the
> IFD
> > linked list just to count the total number of image planes (unless we
> could
> > obtain that information in some other format-specific way), but it would
> > probably be faster than parsing all IFDs fully up-front.
> >
> > We think that Bio-Formats could deliver the best of both worlds
> > (correctness and performance), if we added some heuristics along these
> > lines in common cases. It could make a big difference in usability.
> >
> > Do other Bio-Formats devs agree? If so, I can file a ticket on the OME
> Trac
> > for it, if one doesn't already exist.
> >
> > Regards,
> > Curtis
>
> > _______________________________________________
> > ome-devel mailing list
> > ome-devel at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20121101/5c1ca2e1/attachment.html>